The long-term neuroimaging correlates of clinical recovery have not been described in anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis. The aim of the study is to evaluate the long-term outcome of brain atrophy in anti-NMDAR encephalitis. Patients were two women (ages 17 and 33 years) with severe anti-NMDAR encephalitis resulting in decreased level of consciousness, autonomic instability, hypoventilation, and dyskinesias requiring continuous infusion of anesthetic agents for 6-7 months. Brain MRI and cerebral blood flow SPECT obtained at the time of maximal neurological disability were compared with similar studies obtained 5-7 years later. Both patients were hospitalized for 9-14 months and developed frontotemporal atrophy and hypoperfusion 7-12 months after symptom presentation. In both patients, cognitive functions gradually improved over the next 4-5 years. Comparative neuroimaging studies obtained 5-7 years after symptom presentation showed dramatic improvement of the atrophy and frontotemporal hypoperfusion. The severe and protracted deficits and the frontotemporal atrophy that occur in some patients with anti-NMDAR encephalitis are potentially reversible. This suggests that a functional rather than a structural neuronal damage underlies the pathogenesis of this disorder.